A first-generation X-inactivation profile of the human X chromosome

TLDR

In females, most X‑chromosome genes are assumed to be transcriptionally silenced on the inactive X, but many human genes escape inactivation and are expressed from both Xa and Xi, reflecting distinct epigenetic responses and potential phenotypic effects of X aneuploidy. The study aims to identify genes that escape X inactivation and produce a first‑generation X‑inactivation profile by reverse‑transcription PCR of 224 X‑linked transcripts in mouse/human hybrids, with the goal of informing clinical genetics, counseling, and understanding of X‑chromosome organization. The authors used reverse‑transcription PCR to assess expression of 224 X‑linked genes in multiple mouse/human somatic cell hybrids that contain a normal human Xi but lack an Xa. The survey, covering about 10% of X‑linked transcripts, identified 34 genes (including three pseudoautosomal) that escape inactivation, most of which (31/34) map to Xp, indicating a nonrandom distribution and suggesting that Xp imbalance may have greater clinical impact than Xq.

Abstract

In females, most genes on the X chromosome are generally assumed to be transcriptionally silenced on the inactive X as a result of X inactivation. However, particularly in humans, an increasing number of genes are known to “escape” X inactivation and are expressed from both the active (Xa) and inactive (Xi) X chromosomes; such genes reflect different molecular and epigenetic responses to X inactivation and are candidates for phenotypes associated with X aneuploidy. To identify genes that escape X inactivation and to generate a first-generation X-inactivation profile of the X, we have evaluated the expression of 224 X-linked genes and expressed sequence tags by reverse-transcription–PCR analysis of a panel of multiple independent mouse/human somatic cell hybrids containing a normal human Xi but no Xa. The resulting survey yields an initial X-inactivation profile that is estimated to represent ≈10% of all X-linked transcripts. Of the 224 transcripts tested here, 34 (three of which are pseudoautosomal) were expressed in as many as nine Xi hybrids and thus appear to escape inactivation. The genes that escape inactivation are distributed nonrandomly along the X; 31 of 34 such transcripts map to Xp, implying that the two arms of the X are epigenetically and/or evolutionarily distinct and suggesting that genetic imbalance of Xp may be more severe clinically than imbalance of Xq. A complete X-inactivation profile will provide information relevant to clinical genetics and genetic counseling and should yield insight into the genomic and epigenetic organization of the X chromosome.